Non-linear errors introduced by a non-polarized beam splitter considerably impact the measurement accuracy of an interferometer. Therefore, it is necessary to measure phase shift characteristics introduced by the non-polarized beam splitter and explore the compensation method of the non-polarized beam splitter. Based on the Jones matrix method describing polarization states, we set up a measurement system for the transmission and reflection phase shifts of the non-polarized beam splitter and the effective compensation of the reflection phase shifts. In addition, the temperature characteristics of the phase shifts are experimentally investigated. The aforementioned system uses the balanced detection method of dual photo-detectors; this method exhibits high detection accuracy, good stability, and anti-interference and can also eliminate the fluctuation in light power. The results show that the reflection phase shift of the non-polarized beam splitter is larger than the transmission phase shift, and the overall phase shift is effectively reduced by combining two non-polarized beam splitters with almost the same reflection phase shifts. Moreover, the phase shift changes with a change in temperature. An inflection point of the minimum phase shift in the temperature characteristic curve is observed, which helps determine the optimal operating temperature of the non-polarized beam splitter.